7-97872310-TGGCGCGGGGCGCAG-TGGCGCGGGGCGCAGGGCGCAGGGCGCGGGGCGCAG

Variant names:

• chr7-97872323-A-AGGGCGCAGGGCGCGGGGCGCA
• NM_001673.5:c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC

Variant summary

Our verdict is Uncertain significance. The variant received 0 ACMG points: 0P and 0B.

The NM_001673.5(ASNS):​c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC variant causes a intron change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. It is difficult to determine the true allele frequency of this variant because it is of type INS_BIG, and the frequency of such variant types in population databases may be underestimated and unreliable. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.

• Frequency: Genomes: not found (cov: 35)
• Consequence: ASNS NM_001673.5 intron
• Clinical Significance: Not reported in ClinVar
• Conservation: PhyloP100: -0.201
• Publications: 0 publications found

Genes affected

ASNS (HGNC:753): (asparagine synthetase (glutamine-hydrolyzing)) The protein encoded by this gene is involved in the synthesis of asparagine. This gene complements a mutation in the temperature-sensitive hamster mutant ts11, which blocks progression through the G1 phase of the cell cycle at nonpermissive temperature. Alternatively spliced transcript variants have been described for this gene. [provided by RefSeq, May 2010]

ASNS Gene-Disease associations (from GenCC):

• congenital microcephaly - severe encephalopathy - progressive cerebral atrophy syndrome

  Inheritance: AR Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, ClinGen, Labcorp Genetics (formerly Invitae), G2P

ENSG00000297732 (HGNC:):

ACMG classification

Our verdict: Uncertain_significance. The variant received 0 ACMG points.

Variant Effect in Transcripts

ACMG analysis was done for transcript: NM_001673.5. You can select a different transcript below to see updated ACMG assignments.

RefSeq Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASNS	NM_001673.5	MANE Select	c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	NP_001664.3
	ASNS	NM_001352496.2		c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	NP_001339425.1	P08243-1
	ASNS	NM_183356.4		c.-338+27_-338+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	NP_899199.2	P08243-1

Ensembl Transcripts

Sel.	Gene	Transcript	Tags	HGVSc	HGVSp	Effect	Exon Rank	Protein	UniProt
	ASNS	ENST00000394308.8	TSL:1 MANE Select	c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	ENSP00000377845.3	P08243-1
	ASNS	ENST00000175506.8	TSL:1	c.-338+27_-338+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	ENSP00000175506.4	P08243-1
	ASNS	ENST00000931349.1		c.-60+27_-60+28insTGCGCCCCGCGCCCTGCGCCC		intron	N/A	ENSP00000601408.1

Frequencies

GnomAD3 genomes Cov.: 35

GnomAD4 exome Cov.: 0

GnomAD4 genome Cov.: 35

ClinVar

Not reported in ClinVar

Computational scores

Source: dbNSFP v4.9

Name	Calibrated prediction	Score	Prediction
PhyloP100		-0.20

Splicing

Find out detailed SpliceAI scores and Pangolin per-transcript scores at spliceailookup.broadinstitute.org

MaxEntScan Visualizer can be used to analyze the impact of this mutation on the neighboring sequence.

Other links and lift over

hg19: chr7-97501635;